Dynamics of activation in the voltage-sensing domain of <i>Ciona intestinalis</i> phosphatase Ci-VSP

The Ciona intestinalis voltage-sensing phosphatase (Ci-VSP) is a membrane protein containing a voltage-sensing domain (VSD) that is homologous to VSDs from voltage-gated ion channels responsible for cellular excitability. Previously published crystal structures of Ci-VSD in putative resting and active conformations suggested a helical-screw voltage sensing mechanism in which the S4 helix translocates and rotates to enable exchange of salt-bridge partners, but the microscopic details of the transition between the resting and active conformations remained unknown. Here, by combining extensive molecular dynamics simulations with a recently developed computational framework based on dynamical operators, we elucidate the microscopic mechanism of the resting-active transition at physiological membrane potential. Sparse regression reveals a small set of coordinates that distinguish intermediates that are hidden from electrophysiological measurements. The intermediates arise from a noncanonical helical-screw mechanism in which translocation, rotation, and side-chain movement of the S4 helix are only loosely coupled. These results provide insights into existing experimental and computational findings on voltage sensing and suggest ways of further probing its mechanism

Accurate estimates of dynamical statistics using memory

Many chemical reactions and molecular processes occur on timescales that are significantly longer than those accessible by direct simulation. One successful approach to estimating dynamical statistics for such processes is to use many short time series observations of the system to construct a Markov state model (MSM), which approximates the dynamics of the system as memoryless transitions between a set of discrete states. The dynamical Galerkin approximation (DGA) generalizes MSMs for the problem of calculating dynamical statistics, such as committors and mean first passage times, by replacing the set of discrete states with a projection onto a basis. Because the projected dynamics are generally not memoryless, the Markov approximation can result in significant systematic error. Inspired by quasi-Markov state models, which employ the generalized master equation to encode memory resulting from the projection, we reformulate DGA to account for memory and analyze its performance on two systems: a two-dimensional triple well and helix-to-helix transitions of the AIB$_9$ peptide. We demonstrate that our method is robust to the choice of basis and can decrease the time series length required to obtain accurate kinetics by an order of magnitude.Comment: 17 pages, 14 figure

Inexact iterative numerical linear algebra for neural network-based spectral estimation and rare-event prediction

Understanding dynamics in complex systems is challenging because there are many degrees of freedom, and those that are most important for describing events of interest are often not obvious. The leading eigenfunctions of the transition operator are useful for visualization, and they can provide an efficient basis for computing statistics such as the likelihood and average time of events (predictions). Here we develop inexact iterative linear algebra methods for computing these eigenfunctions (spectral estimation) and making predictions from a data set of short trajectories sampled at finite intervals. We demonstrate the methods on a low-dimensional model that facilitates visualization and a high-dimensional model of a biomolecular system. Implications for the prediction problem in reinforcement learning are discussed.Comment: 27 pages, 16 figure

Spatial sampling of the thermospheric vertical wind field at auroral latitudes

Results are presented from two nights of bistatic Doppler measurements of neutral thermospheric winds using Fabry!Perot spectrometers at Mawson and Davis stations in Antarctica. A scanning Doppler imager (SDI) at Mawson and a narrow-field Fabry-Perot spectrometer (FPS) at Davis have been used to estimate the vertical wind at three locations along the great circle joining the two stations, in addition to the vertical wind routinely observed above each station. These data were obtained from observations of the 630.0 nm airglow line of atomic oxygen, at a nominal altitude of 240 km. Low!resolution all-sky images produced by the Mawson SDI have been used to relate disturbances in the measured vertical wind field to auroral activity and divergence in the horizontal wind field. Correlated vertical wind responses were observed on a range of horizontal scales from ~150 to 480 km. In general, the behavior of the vertical wind was in agreement with earlier studies, with strong upward winds observed poleward of the optical aurora and sustained, though weak, downward winds observed early in the night. The relation between vertical wind and horizontal divergence was seen to follow the general trend predicted by Burnside et al. (1981), whereby upward vertical winds were associated with positive divergence and vice versa; however, a scale height approximately 3–4 times greater than that modeled by NRLMSISE-00 was required to best fit the data using this relation

General SU(2)L×SU(2)R×U(1)EMSU(2)_L\times SU(2)_R \times U(1)_{EM} Sigma Model With External Sources, Dynamical Breaking And Spontaneous Vacuum Symmetry Breaking

We give a general $SU(2)_L\times SU(2)_R$ $\times U(1)_{EM}$ sigma model with external sources, dynamical breaking and spontaneous vacuum symmetry breaking, and present the general formulation of the model. It is found that $\sigma$ and $\pi ^0$ without electric charges have electromagnetic interaction effects coming from their internal structure. A general Lorentz transformation relative to external sources $J_{gauge}$ $=(J_{A_\mu},J_{A_\mu ^\kappa})$ is derived, using the general Lorentz transformation and the four-dimensional current of nuclear matter of the ground state with $J_{gauge}$ = 0, we give the four-dimensional general relations between the different currents of nuclear matter systems with $J_{gauge}\neq 0$ and those with $J_{gauge}=0$. The relation of the density's coupling with external magnetic field is derived, which conforms well to dense nuclear matter in a strong magnetic field. We show different condensed effects in strong interaction about fermions and antifermions, and give the concrete scalar and pseudoscalar condensed expressions of $\sigma_0$ and $\pi_0$ bosons. About different dynamical breaking and spontaneous vacuum symmetry breaking, the concrete expressions of different mass spectra are obtained in field theory. This paper acquires the running spontaneous vacuum breaking value $\sigma_0^{\prime},$ and obtains the spontaneous vacuum breaking in terms of the running $\sigma_0^{\prime}$, which make nucleon, $\sigma$ and $\pi$ particles gain effective masses. We achieve both the effect of external sources and nonvanishing value of the condensed scalar and pseudoscalar paticles. It is deduced that the masses of nucleons, $\sigma$ and $\pi$ generally depend on different external sources.Comment: 12 page

The repulsive lattice gas, the independent-set polynomial, and the Lov\'asz local lemma

We elucidate the close connection between the repulsive lattice gas in equilibrium statistical mechanics and the Lovasz local lemma in probabilistic combinatorics. We show that the conclusion of the Lovasz local lemma holds for dependency graph G and probabilities {p_x} if and only if the independent-set polynomial for G is nonvanishing in the polydisc of radii {p_x}. Furthermore, we show that the usual proof of the Lovasz local lemma -- which provides a sufficient condition for this to occur -- corresponds to a simple inductive argument for the nonvanishing of the independent-set polynomial in a polydisc, which was discovered implicitly by Shearer and explicitly by Dobrushin. We also present some refinements and extensions of both arguments, including a generalization of the Lovasz local lemma that allows for "soft" dependencies. In addition, we prove some general properties of the partition function of a repulsive lattice gas, most of which are consequences of the alternating-sign property for the Mayer coefficients. We conclude with a brief discussion of the repulsive lattice gas on countably infinite graphs.Comment: LaTex2e, 97 pages. Version 2 makes slight changes to improve clarity. To be published in J. Stat. Phy

Planck Intermediate Results. IX. Detection of the Galactic haze with Planck

Using precise full-sky observations from Planck, and applying several methods of component separation, we identify and characterize the emission from the Galactic "haze" at microwave wavelengths. The haze is a distinct component of diffuse Galactic emission, roughly centered on the Galactic centre, and extends to |b| ~35 deg in Galactic latitude and |l| ~15 deg in longitude. By combining the Planck data with observations from the WMAP we are able to determine the spectrum of this emission to high accuracy, unhindered by the large systematic biases present in previous analyses. The derived spectrum is consistent with power-law emission with a spectral index of -2.55 +/- 0.05, thus excluding free-free emission as the source and instead favouring hard-spectrum synchrotron radiation from an electron population with a spectrum (number density per energy) dN/dE ~ E^-2.1. At Galactic latitudes |b|<30 deg, the microwave haze morphology is consistent with that of the Fermi gamma-ray "haze" or "bubbles," indicating that we have a multi-wavelength view of a distinct component of our Galaxy. Given both the very hard spectrum and the extended nature of the emission, it is highly unlikely that the haze electrons result from supernova shocks in the Galactic disk. Instead, a new mechanism for cosmic-ray acceleration in the centre of our Galaxy is implied.Comment: 15 pages, 9 figures, submitted to Astronomy and Astrophysic

First narrow-band search for continuous gravitational waves from known pulsars in advanced detector data

Spinning neutron stars asymmetric with respect to their rotation axis are potential sources of continuous gravitational waves for ground-based interferometric detectors. In the case of known pulsars a fully coherent search, based on matched filtering, which uses the position and rotational parameters obtained from electromagnetic observations, can be carried out. Matched filtering maximizes the signalto- noise (SNR) ratio, but a large sensitivity loss is expected in case of even a very small mismatch between the assumed and the true signal parameters. For this reason, narrow-band analysis methods have been developed, allowing a fully coherent search for gravitational waves from known pulsars over a fraction of a hertz and several spin-down values. In this paper we describe a narrow-band search of 11 pulsars using data from Advanced LIGO’s first observing run. Although we have found several initial outliers, further studies show no significant evidence for the presence of a gravitational wave signal. Finally, we have placed upper limits on the signal strain amplitude lower than the spin-down limit for 5 of the 11 targets over the bands searched; in the case of J1813-1749 the spin-down limit has been beaten for the first time. For an additional 3 targets, the median upper limit across the search bands is below the spin-down limit. This is the most sensitive narrow-band search for continuous gravitational waves carried out so far

Hunt for new phenomena using large jet multiplicities and missing transverse momentum with ATLAS in 4.7 fb−1 of s√=7TeV proton-proton collisions

Results are presented of a search for new particles decaying to large numbers of jets in association with missing transverse momentum, using 4.7 fb−1 of pp collision data at s√=7TeV collected by the ATLAS experiment at the Large Hadron Collider in 2011. The event selection requires missing transverse momentum, no isolated electrons or muons, and from ≥6 to ≥9 jets. No evidence is found for physics beyond the Standard Model. The results are interpreted in the context of a MSUGRA/CMSSM supersymmetric model, where, for large universal scalar mass m 0, gluino masses smaller than 840 GeV are excluded at the 95% confidence level, extending previously published limits. Within a simplified model containing only a gluino octet and a neutralino, gluino masses smaller than 870 GeV are similarly excluded for neutralino masses below 100 GeV

Expected Performance of the ATLAS Experiment - Detector, Trigger and Physics

A detailed study is presented of the expected performance of the ATLAS detector. The reconstruction of tracks, leptons, photons, missing energy and jets is investigated, together with the performance of b-tagging and the trigger. The physics potential for a variety of interesting physics processes, within the Standard Model and beyond, is examined. The study comprises a series of notes based on simulations of the detector and physics processes, with particular emphasis given to the data expected from the first years of operation of the LHC at CERN